Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE DROSOPHILA INITIATOR CASPASE DRONC
 
Authors :  N. Yan, L. Gu, Y. Shi
Date :  15 Jan 06  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Caspase, Apoptosis, Initiator Caspase Activation, Dimerization, Active Site Conformation, Hydrolysis/Apoptosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Yan, J. R. Huh, V. Schirf, B. Demeler, B. A. Hay, Y. Shi
Structure And Activation Mechanism Of The Drosophila Initiator Caspase Dronc
J. Biol. Chem. V. 281 8667 2006
PubMed-ID: 16446367  |  Reference-DOI: 10.1074/JBC.M513232200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASPASE NC
    ChainsA
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentDRONC RESIDUES 136-450
    GeneNC
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2FP3)

(-) Sites  (0, 0)

(no "Site" information available for 2FP3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FP3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FP3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FP3)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.DRONC_DROME194-322  1A:194-317
2CASPASE_CYSPS01122 Caspase family cysteine active site.DRONC_DROME309-320  1A:309-317
3CASPASE_P10PS50207 Caspase family p10 domain profile.DRONC_DROME357-445  1A:358-445

(-) Exons   (0, 0)

(no "Exon" information available for 2FP3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:254
 aligned with DRONC_DROME | Q9XYF4 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:293
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446   
          DRONC_DROME   157 ALTPYVGVVDGPEVKKSKKIHGGDSAILGTYKMQSRFNRGVLLMVNIMDYPDQNRRRIGAEKDSKSLIHLFQELNFTIFPYGNVNQDQFFKLLTMVTSSSYVQNTECFVMVLMTHGNSVEGKEKVEFCDGSVVDMQKIKDHFQTAKCPYLVNKPKVLMFPFCRGDEYDLGHPKNQGNLMEPVYTAQEEKWPDTQTEGIPSPSTNVPSLADTLVCYANTPGYVTHRDLDTGSWYIQKFCQVMADHAHDTDLEDILKKTSEAVGNKRTKKGSMQTGAYDNLGFNKKLYFNPGFFN 449
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................eeeeeee............hhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhhhhhhh..eeeeee..ee......eee.....eeehhhhhhh.....hhhhh...eeeee...---------------------------------------.........eeeee............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...........eeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------CASPASE_P20  PDB: A:194-317 UniProt: 194-322                                                                                     ----------------------------------CASPASE_P10  PDB: A:358-445 UniProt: 357-445                                             ---- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------CASPASE_CYS --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fp3 A 157 ALTPYVGVVDGPEVKKSKKIHGGDSAILGTYKMQSRFNRGVLLMVNIMDYPDQNRRRIGAEKDSKSLIHLFQELNFTIFPYGNVNQDQFFKLLTMVTSSSYVQNTECFVMVLMTHGNSVEGKEKVEFRDGSVVDMQKIKDHFQTAKCPYLVNKPKVLMFPFA---------------------------------------STNVPSLADTLVCYANTPGYVTHRDLDTGSWYIQKFCQVMADHAHDTDLEDILKKTSEAVGNKRTKKGSMQTGAYDNLGFNKKLYFNPGFFN 449
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316 |       -         -         -         - |     366       376       386       396       406       416       426       436       446   
                                                                                                                                                                                           318                                     358                                                                                           

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2FP3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FP3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FP3)

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DRONC_DROME | Q9XYF4)
molecular function
    GO:0050700    CARD domain binding    Interacting selectively and non-covalently with a CARD (N-terminal caspase recruitment) domain, a protein-protein interaction domain that belongs to the death domain-fold superfamily. These protein molecule families are similar in structure with each consisting of six or seven anti-parallel alpha-helices that form highly specific homophilic interactions between signaling partners. CARD exists in the N-terminal prodomains of several caspases and in apoptosis-regulatory proteins and mediates the assembly of CARD-containing proteins that participate in activation or suppression of CARD carrying members of the caspase family.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0097199    cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile, and contributing to the apoptotic signaling pathway.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0097190    apoptotic signaling pathway    A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
    GO:0048102    autophagic cell death    A form of programmed cell death that is accompanied by the formation of autophagosomes. Autophagic cell death is characterized by lack of chromatin condensation and massive vacuolization of the cytoplasm, with little or no uptake by phagocytic cells.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0048749    compound eye development    The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0035234    ectopic germ cell programmed cell death    Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo.
    GO:0001700    embryonic development via the syncytial blastoderm    The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster.
    GO:0008258    head involution    Movement of the anterior ectoderm to the interior of the embryo.
    GO:0007516    hemocyte development    The process whose specific outcome is the progression of the hemocyte over time, from its formation to the mature structure. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen.
    GO:0035006    melanization defense response    The blackening of the wounded area of the cuticle or the surface of invading pathogens, parasites or parasitoids, resulting from a proteolytic cascade leading to the de novo synthesis and deposition of melanin.
    GO:0007552    metamorphosis    A biological process in which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's form or structure. Examples include the change from tadpole to frog, and the change from larva to adult. An example of this is found in Drosophila melanogaster.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0016322    neuron remodeling    The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development.
    GO:0045476    nurse cell apoptotic process    Any apoptotic process in a nurse cell. During late oogenesis, following the transfer of substances from the nurse cells to the oocyte, nurse cell remnants are cleared from the egg chamber by apoptotic process.
    GO:0046672    positive regulation of compound eye retinal cell programmed cell death    Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
    GO:2001269    positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    GO:0010623    programmed cell death involved in cell development    The activation of endogenous cellular processes that result in the death of a cell as part of its development.
    GO:0016540    protein autoprocessing    Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
    GO:0051291    protein heterooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0010941    regulation of cell death    Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0046668    regulation of retinal cell programmed cell death    Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina.
    GO:0035071    salivary gland cell autophagic cell death    The stage-specific programmed cell death of salivary gland cells during salivary gland histolysis.
    GO:0035070    salivary gland histolysis    The stage-specific break down of the larval salivary glands during Drosophila metamorphosis, to allow replacement of larval structures by tissues and structures that form the adult fly.
    GO:0007423    sensory organ development    The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure.
    GO:0007291    sperm individualization    The resolution of the male germline syncytium or cyst into individual gametes by packaging each spermatid into its own plasma membrane.
    GO:0031638    zymogen activation    The proteolytic processing of an inactive enzyme to an active form.
cellular component
    GO:0043293    apoptosome    A multisubunit protein complex involved in the signaling phase of the apoptotic process. In mammals it is typically composed of seven Apaf-1 subunits bound to cytochrome c and caspase-9. A similar complex to promote apoptosis is formed from homologous gene products in other eukaryotic organisms.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2fp3)
 
  Sites
(no "Sites" information available for 2fp3)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2fp3)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2fp3
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DRONC_DROME | Q9XYF4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.22.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DRONC_DROME | Q9XYF4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DRONC_DROME | Q9XYF41q4q 3j9k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2FP3)